Reinstate brainmapper ci check (#347)

* Reinstate brainmapper CLI check

* Update README to point to brainmapper pages

* Update install instructions

* Drop python 3.8 support

* Fix rebase barfs

* pre-commit pass

.github/workflows/test_and_deploy.yml

@@ -40,7 +40,7 @@ jobs:
       matrix:
         # Run all supported Python versions on linux
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
         # Include one windows, one macos run
         include:
         - os: macos-latest
@@ -92,43 +92,42 @@ jobs:
 
   # Run brainglobe-workflows brainmapper-CLI tests to check for
   # breakages
-  # test_brainmapper_cli:
-  #   needs: [linting, manifest]
-  #   name: Run brainmapper tests to check for breakages
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Cache tensorflow model
-  #       uses: actions/cache@v3
-  #       with:
-  #         path: "~/.cellfinder"
-  #         key: models-${{ hashFiles('~/.cellfinder/**') }}
+  test_brainmapper_cli:
+    needs: [linting, manifest]
+    name: Run brainmapper tests to check for breakages
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cache tensorflow model
+        uses: actions/cache@v3
+        with:
+          path: "~/.cellfinder"
+          key: models-${{ hashFiles('~/.cellfinder/**') }}
 
-  #     - name: Checkout brainglobe-workflows
-  #       uses: actions/checkout@v3
-  #       with:
-  #         repository: 'brainglobe/brainglobe-workflows'
+      - name: Checkout brainglobe-workflows
+        uses: actions/checkout@v3
+        with:
+          repository: 'brainglobe/brainglobe-workflows'
 
-  #     - name: Set up Python 3.10
-  #       uses: actions/setup-python@v3
-  #       with:
-  #         python-version: "3.10"
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
 
-  #     - name: Install test dependencies
-  #       run: |
-  #         python -m pip install --upgrade pip wheel
-  #         # Install latest SHA on this brainglobe-workflows branch
-  #         python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA
-  #         # Install checked out copy of brainglobe-workflows
-  #         python -m pip install .[dev]
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          # Install latest SHA on this brainglobe-workflows branch
+          python -m pip install git+$GITHUB_SERVER_URL/$GITHUB_REPOSITORY@$GITHUB_SHA
+          # Install checked out copy of brainglobe-workflows
+          python -m pip install .[dev]
 
-  #     - name: Run brainmapper tests in brainglobe-workflows
-  #       run: |
-  #         python -m pytest --color=yes -v tests/brainmapper
+      - name: Run brainmapper tests in brainglobe-workflows
+        run: |
+          python -m pytest --color=yes -v tests/brainmapper
 
   build_sdist_wheel:
     name: Build source distribution and wheel
-    # needs: [test, test_brainmapper_cli, test_numba_disabled]
-    needs: [test]
+    needs: [test, test_brainmapper_cli, test_numba_disabled]
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:

README.md

@@ -19,21 +19,31 @@ For more details, head over to [the documentation website](https://brainglobe.in
 
 At a glance:
 
-- There is a [command-line interface](https://brainglobe.info/documentation/cellfinder/user-guide/command-line/index.html) that integrates [with `brainreg`](https://github.com/brainglobe/brainreg) for automated cell detection and classification.
+- There is a command-line interface called [brainmapper](https://brainglobe.info/documentation/brainglobe-workflows/brainmapper/index.html) that integrates [with `brainreg`](https://github.com/brainglobe/brainreg) for automated cell detection and classification. You can install it through [`brainglobe-workflows`](https://brainglobe.info/documentation/brainglobe-workflows/index.html).
 - There is a [napari plugin](https://brainglobe.info/documentation/cellfinder/user-guide/napari-plugin/index.html) for interacting graphically with the cellfinder tool.
 - There is a [Python API](https://brainglobe.info/documentation/cellfinder/user-guide/cellfinder-core.html) to allow users to integrate BrainGlobe tools into their custom workflows.
 
 ## Installation
 
 You can find [the installation instructions](https://brainglobe.info/documentation/cellfinder/installation.html#installation) on the BrainGlobe website, which will go into more detail about the installation process if you want to minimise your installation to suit your needs.
-However, we recommend that users install `cellfinder` either through installing BrainGlobe version 1, or (if you also want the command-line interface) installing `brainglobe-workflows`:
+However, we recommend that users install `cellfinder` either through installing BrainGlobe version 1, or (if you also want the command-line interface) installing `brainglobe-workflows`.
 
 ```bash
-pip install cellfinder>=1.0.0 # If you just want the napari plugin and Python API
-pip install brainglobe>=1.0.0 # If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command
-pip install brainglobe-workflows>=1.0.0 # If you want to include the CLI
+# If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command:
+pip install brainglobe>=1.0.0
+# If you want to install the brainmapper CLI tool as well:
+pip install brainglobe-workflows>=1.0.0
 ```
 
+If you only want the `cellfinder` package by itself, you can `pip install` it alone:
+
+```bash
+pip install cellfinder>=1.0.0
+```
+
+Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
+See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
+
 ## Contributing
 
 If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).

pyproject.toml

@@ -19,7 +19,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     "brainglobe-utils",
     "dask[array]",